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Yorodumi- PDB-4nmx: PCSK9(deltaCRD) in complex with phage-derived inhibitory peptide 2-8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nmx | ||||||
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Title | PCSK9(deltaCRD) in complex with phage-derived inhibitory peptide 2-8 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / subtlisin / receptor degradation / LDL receptor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding ...negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / signaling receptor inhibitor activity / very-low-density lipoprotein particle receptor binding / negative regulation of low-density lipoprotein receptor activity / negative regulation of receptor internalization / endolysosome membrane / regulation of signaling receptor activity / sodium channel inhibitor activity / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / COPII-coated ER to Golgi transport vesicle / apolipoprotein binding / positive regulation of receptor internalization / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / phospholipid metabolic process / regulation of neuron apoptotic process / VLDLR internalisation and degradation / cellular response to starvation / cholesterol metabolic process / neurogenesis / liver development / cholesterol homeostasis / kidney development / Post-translational protein phosphorylation / neuron differentiation / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / : / late endosome / lysosome / early endosome / lysosomal membrane / endoplasmic reticulum lumen / serine-type endopeptidase activity / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / RNA binding / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Eigenbrot, C. / Shia, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Identification of a Small Peptide That Inhibits PCSK9 Protein Binding to the Low Density Lipoprotein Receptor. Authors: Zhang, Y. / Eigenbrot, C. / Zhou, L. / Shia, S. / Li, W. / Quan, C. / Tom, J. / Moran, P. / Di Lello, P. / Skelton, N.J. / Kong-Beltran, M. / Peterson, A. / Kirchhofer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nmx.cif.gz | 165.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nmx.ent.gz | 128 KB | Display | PDB format |
PDBx/mmJSON format | 4nmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/4nmx ftp://data.pdbj.org/pub/pdb/validation_reports/nm/4nmx | HTTPS FTP |
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-Related structure data
Related structure data | 2qtwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14006.670 Da / Num. of mol.: 1 / Fragment: propeptide (UNP residues 31-152) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NARC1, PCSK9, PSEC0052 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NBP7 |
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#2: Protein | Mass: 32836.910 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 153-452) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NARC1, PCSK9, PSEC0052 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
#3: Protein/peptide | Mass: 1698.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide library displayed on M13 phage |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.32 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M lithium chloride, 10% w/v PEG6000, 0.05 M Tris, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 11, 2011 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 39638 / Num. obs: 39638 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.099 / Net I/σ(I): 11 |
Reflection shell | Highest resolution: 1.85 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QTW Resolution: 1.85→37.42 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.636 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.627 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→37.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.95 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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